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Open data
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Basic information
Entry | Database: PDB / ID: 1g9o | ||||||
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Title | FIRST PDZ DOMAIN OF THE HUMAN NA+/H+ EXCHANGER REGULATORY FACTOR | ||||||
![]() | NHE-RF | ||||||
![]() | SIGNALING PROTEIN / PDZ domain / NHERF / COMPLEX | ||||||
Function / homology | ![]() import across plasma membrane / channel activator activity / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / dopamine receptor binding / renal phosphate ion absorption / gamma-aminobutyric acid transmembrane transporter activity / gamma-aminobutyric acid import ...import across plasma membrane / channel activator activity / regulation of renal phosphate excretion / renal sodium ion transport / type 2 metabotropic glutamate receptor binding / glutathione transport / dopamine receptor binding / renal phosphate ion absorption / gamma-aminobutyric acid transmembrane transporter activity / gamma-aminobutyric acid import / cerebrospinal fluid circulation / microvillus assembly / positive regulation of monoatomic ion transmembrane transport / negative regulation of sodium ion transport / bile acid secretion / maintenance of epithelial cell apical/basal polarity / plasma membrane organization / stereocilium tip / intracellular phosphate ion homeostasis / cilium organization / gland morphogenesis / myosin II binding / phospholipase C-activating dopamine receptor signaling pathway / growth factor receptor binding / establishment of Golgi localization / fibroblast migration / type 3 metabotropic glutamate receptor binding / plasma membrane protein complex / establishment of epithelial cell apical/basal polarity / negative regulation of fibroblast migration / negative regulation of platelet-derived growth factor receptor signaling pathway / chloride channel regulator activity / auditory receptor cell stereocilium organization / nuclear migration / regulation of protein kinase activity / microvillus membrane / regulation of cell size / renal absorption / microvillus / transport across blood-brain barrier / negative regulation of mitotic cell cycle / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / phosphatase binding / endomembrane system / beta-2 adrenergic receptor binding / positive regulation of intrinsic apoptotic signaling pathway / protein-membrane adaptor activity / sperm midpiece / ruffle / filopodium / protein localization to plasma membrane / cell periphery / PDZ domain binding / morphogenesis of an epithelium / brush border membrane / sensory perception of sound / negative regulation of canonical Wnt signaling pathway / negative regulation of ERK1 and ERK2 cascade / beta-catenin binding / Wnt signaling pathway / adenylate cyclase-activating dopamine receptor signaling pathway / : / actin cytoskeleton / regulation of cell shape / actin cytoskeleton organization / protein-containing complex assembly / vesicle / transmembrane transporter binding / apical plasma membrane / negative regulation of cell population proliferation / signaling receptor binding / protein-containing complex binding / perinuclear region of cytoplasm / extracellular exosome / membrane / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Karthikeyan, S. / Leung, T. / Birrane, G. / Webster, G. / Ladias, J.A.A. | ||||||
![]() | ![]() Title: Crystal structure of the PDZ1 domain of human Na(+)/H(+) exchanger regulatory factor provides insights into the mechanism of carboxyl-terminal leucine recognition by class I PDZ domains. Authors: Karthikeyan, S. / Leung, T. / Birrane, G. / Webster, G. / Ladias, J.A. #1: ![]() Title: NHE-RF, a regulatory cofactor for Na(+)-H+ exchange, is a common interactor for merlin and ERM (MERM) proteins; Authors: MURTHY, A. / GONZALEZ-AGOSTI, C. / CORDERO, E. / PINNEY, D. / CANDIA, C. / SOLOMON, F. / GUSELLA, J. / RAMESH, V. #2: ![]() Title: Crystal structure of the hCASK PDZ domain reveals the structural basis of class II PDZ domain target recognition Authors: Daniels, D.L. / Cohen, A.R. / Anderson, J.M. / Brunger, A.T. #3: ![]() Title: Crystal structures of a complexed and peptide-free membrane protein-binding domain:Molecular basis of peptide recognition by PDZ Authors: Doyle, D.A. / Lee, A. / Lewis, J. / Kim, E. / Sheng, M. / MacKinnon, R. #4: ![]() Title: Crystal structure of a PDZ domain Authors: Morais Cabral, J.H. / Petosa, C. / Sutcliffe, M.J. / Raza, S. / Byron, O. / Poy, F. / Marfatia, S.M. / Chishti, A.H. / Liddington, R.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 32.8 KB | Display | ![]() |
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PDB format | ![]() | 21.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 410.8 KB | Display | ![]() |
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Full document | ![]() | 411.9 KB | Display | |
Data in XML | ![]() | 7.4 KB | Display | |
Data in CIF | ![]() | 9.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 10043.504 Da / Num. of mol.: 1 / Fragment: PDZ1 DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.9 Details: potassium sodium tartrate, sodium citrate, ammonium sulfate, manganese chloride, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2000 / Details: DUAL SLITS |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98401 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→36 Å / Num. all: 14916 / Num. obs: 14916 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 16.5 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 3.9 / Net I/σ(I): 35 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 10.3 / Num. unique all: 1449 / Rsym value: 15.2 / % possible all: 98.9 |
Reflection | *PLUS Num. measured all: 246628 |
Reflection shell | *PLUS % possible obs: 98.9 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.19 Å2 / ksol: 0.4078 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→24.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.181 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 16.7 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.232 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.189 |